Origin IGS: ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttaactccataaaaattatttgaaaagaagaaaaatttttcccctttcataattattatagaaattgtttgtaatagatagtaaaattttaataaaataggaattttctcacctttttttcatatgattttgtaagaaattacgcttgaattcccttaaaagctattgtataatgactttatgttaaacaagcaaagaaag Mask Tandem Repeat Region ================================================ ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Find is-nt database================================================ Query_seq: TDE2706:TDE2707|TDE2706:TDE2707:hypothetical protein:hypothetical protein:<-->:2753884..2754086 203 ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2706:TDE2707|TDE2706:TDE2707:hypothetical protein:hypothetical protein:<-->:2753884..2754086 203 ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2706:TDE2707|TDE2706:TDE2707:hypothetical protein:hypothetical protein:<-->:2753884..2754086 203 ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 98 End: 202 ................................................................................................. M P I L L K F Y Y L L Q T I S I I I M K G E K F F F F S N N F Y G V K . ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 28 End: 57 ...........................CTTGAATTCCCTTAAAAGCTATTGTATAAT.................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 115 End: 144 ..................................................................................................................ATAGAAATTGTTTGTAATAGATAGTAAAAT........................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2706:TDE2707|TDE2706:TDE2707:hypothetical protein:hypothetical protein:<-->:2753884..2754086 203 ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_002967_TDE2706_TDE2707|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2753884,2754086]|203 HSP 1 e-value: 6.0E-99 bit: 361.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgnnnnnnnggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa ctttctttgcttgtttaacataaagtcattatacaatagcttttaagggaattcaagcgtaatttcttacaaaatcatatgaaaaaaaggtgagaaaattcctattttattaaaattttactatctattacaaacaatttctataataattatgaaaggggaaaaatttttcttcttttcaaataatttttatggagttaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCUUUGCUUGUUUAACAUAAAGUCAUUAUACAAUAGCUUUUAAGGGAAUUCAAGCGUAAUUUCUUACAAAAUCAUAUGAAAAAAAGGUGAGAAAAUUCCUAUUUUAUUAAAAUUUUACUAUCUAUUACAAACAAUUUCUAUAAUAAUUAUGAAAGGGGAAAAAUUUUUCUUCUUUUCAAAUAAUUUUUAUGGAGUUAAAA ........(((((..(..(..((((..(((....)))..))))....)..)..)))))....((((((((....((....)).......)))))))).........................................((((((((.(((((((((((((((((....)))))))))))...)))))).))))))))...... (-33.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAACUCCAUAAAAAUUAUUUGAAAAGAAGAAAAAUUUUUCCCCUUUCAUAAUUAUUAUAGAAAUUGUUUGUAAUAGAUAGUAAAAUUUUAAUAAAAUAGGAAUUUUCUCACCUUUUUUUCAUAUGAUUUUGUAAGAAAUUACGCUUGAAUUCCCUUAAAAGCUAUUGUAUAAUGACUUUAUGUUAAACAAGCAAAGAAAG .............((((((((.((((((((((......................((((((((((.....))))))))))..((.((((((((.........))))))))))...)))))))))).))))))))((((....))))(((((.............((....))....((((.....))))..)))))........ (-30.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 740 60 11 151 102 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 572 180 132 210 163 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 554 170 121 219 172 NC_002967:TDE0670|5end_ATP-dependent_protease_La_707938..708168_POSITIVE 433 199 151 78 31 NC_002967:TDE2099|5end_hypothetical_protein_2125027..2125257_POSITIVE 418 188 141 144 99 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 410 158 113 231 186 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 398 160 113 221 174 NC_002967:TDE0164|5end_hypothetical_protein_193998..194228_NEGATIVE 379 178 131 193 146 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 359 146 114 187 155 NC_002967:TDE1990|5end_ATP-dependent_helicase,_DinG_family_2008496..2008726_NEGATIVE 333 178 135 139 96 NC_002967:TDE2719|5end_hypothetical_protein_2776045..2776275_POSITIVE 316 180 135 141 96 NC_002967:TDE0165|5end_hypothetical_protein_194122..194352_POSITIVE 293 180 131 139 94 NC_002967:TDE2136|5end_hypothetical_protein_2165659..2165889_NEGATIVE 268 199 156 47 2 NC_002967:TDE0984|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein,_putative_1009474..1009704_POSITIVE 253 196 153 155 115 NC_002967:TDE0862|5end_hypothetical_protein_883192..883422_POSITIVE 249 197 155 157 118 NC_002967:TDE1344|5end_hypothetical_protein_1382392..1382622_POSITIVE 244 199 155 159 115 NC_002967:TDE0049|5end_hypothetical_protein_59089..59319_NEGATIVE 238 196 153 156 116 NC_002967:TDE0007|5end_hypothetical_protein_9874..10104_POSITIVE 232 125 87 168 134 NC_002967:TDE2216|5end_galactoside_ABC_transporter,_ATP-binding_protein_2256653..2256883_NEGATIVE 232 48 2 128 73 NC_002967:TDE1035|5end_transcriptional_regulator,_PadR_family_1063454..1063684_POSITIVE 220 48 1 170 131 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 146 114 49 17 NC_002967:TDE1991|3end_hypothetical_protein_2008634..2008784_NEGATIVE 232 125 87 57 23 NC_002967:TDE2217|3end_galactose/glucose-binding_lipoprotein_2256764..2256914_NEGATIVE 232 48 2 60 5 NC_002967:TDE1034|3end_magnesium_and_cobalt_transporter,_putative_1063466..1063616_POSITIVE 208 50 9 43 1 NC_002967:TDE2776|3end_proline_iminopeptidase_2828385..2828535_POSITIVE 206 59 11 115 74 NC_002967:TDE0274|3end_ABC_transporter,_ATP-binding/permease_protein_304630..304780_NEGATIVE 200 74 48 36 6 NC_002967:TDE0830|3end_hypothetical_protein_851609..851759_NEGATIVE 200 113 75 52 16 NC_002967:TDE0806|3end_hypothetical_protein_828340..828490_NEGATIVE 197 49 13 134 85 NC_002967:TDE2399|3end_ribonuclease_P_protein_component_2425804..2425954_NEGATIVE 197 43 1 150 100 NC_002967:TDE0222|3end_acetyltransferase,_GNAT_family_254696..254846_NEGATIVE 191 57 25 68 36 NC_002967:TDE2722|3end_carhohydrate_kinase,_FGGY_family_2779666..2779816_NEGATIVE 186 60 11 147 108 NC_002967:TDE1597|3end_transporter,_putative_1646695..1646845_NEGATIVE 186 59 23 56 16 NC_002967:TDE1132|3end_chorismate_synthase_1164580..1164730_POSITIVE 186 58 24 105 73 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 182 70 21 129 74 NC_002967:TDE1569|3end_hypothetical_protein_1619975..1620125_POSITIVE 180 181 157 59 34 NC_002967:TDE1147|3end_hypothetical_protein_1185529..1185679_NEGATIVE 176 62 26 46 3 NC_002967:TDE2585|3end_methyl-accepting_chemotaxis_domain/unknown_domain_protein_2617976..2618126_NEGATIVE 176 79 39 141 107 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 176 43 1 124 85 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 176 172 141 92 64 NC_002967:TDE0323|3end_hypothetical_protein_355750..355900_NEGATIVE 174 54 11 80 36 NC_002967:TDE1289|3end_hypothetical_protein_1327510..1327660_POSITIVE